Re: [AMBER] Interpreting the distance covariance matrix

From: Sergio R Aragon <>
Date: Tue, 14 Jun 2011 22:16:28 +0000

Hello Sajeewa,

Following up on what Mariano Rech has told you, from 22 carbons atoms you would generate a matrix of distances containing 22^2 = 484 numbers. The number of off-diagonal elements for this symmetric matrix is (484-22)/2 = 231. This is equivalent to the formula n(n-1)/2 that Mariano used. Thus we would believe you have 231 different numbers. That is not at all the same as saying you have a 231 x 231 matrix (that would yield 231^2 = 53 361 numbers!). How many numbers do you actually have?


Sergio Aragon

-----Original Message-----
From: Sajeewa Pemasinghe []
Sent: Monday, June 13, 2011 3:49 PM
Subject: [AMBER] Interpreting the distance covariance matrix


I have run a distance-covarinace analysis for 22 alpha carbon atoms
specified by the mask1. I thought I would get a 22 by 22 symmetric matrix
where the diagonal elements correspond to the variances. Instead I got a 231
by 231 symmetric matrix. I am having a very hard time interpreting this.
This is my first time running a distance covariance calculation in amber. I
would really appreciate if you could give me some helpful explanation in
interpreting the structure of 231 by 231 matrix.

Best Regards
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Received on Tue Jun 14 2011 - 15:30:03 PDT
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